/*
   There are a total of 9 entries in the algebraic variable array.
   There are a total of 19 entries in each of the rate and state variable arrays.
   There are a total of 69 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (minute).
 * STATES[0] is Clb2 in component Clb2 (dimensionless).
 * CONSTANTS[0] is epsilon in component Clb2 (dimensionless).
 * CONSTANTS[1] is Jm in component Clb2 (dimensionless).
 * CONSTANTS[2] is ks_clb in component Clb2 (first_order_rate_constant).
 * CONSTANTS[3] is kd_clb_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[4] is kd_clb_2 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[5] is kd_clb_3 in component kinetic_parameters (first_order_rate_constant).
 * ALGEBRAIC[8] is kswe in component kinetic_parameters (first_order_rate_constant).
 * ALGEBRAIC[7] is kmih in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[6] is kass in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[7] is kdiss in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[8] is kd_sic in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[9] is kd_sic_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[10] is kd_sic_2 in component kinetic_parameters (first_order_rate_constant).
 * STATES[1] is M in component M (dimensionless).
 * STATES[2] is Mcm_a in component Mcm_a (dimensionless).
 * STATES[3] is Cdh1_a in component Cdh1_a (dimensionless).
 * STATES[4] is Cdc20_a in component Cdc20_a (dimensionless).
 * STATES[5] is Sic1 in component Sic1 (dimensionless).
 * STATES[6] is PClb2 in component PClb2 (dimensionless).
 * STATES[7] is Trim in component Trim (dimensionless).
 * STATES[8] is Cln in component Cln (dimensionless).
 * STATES[9] is PTrim in component PTrim (dimensionless).
 * CONSTANTS[11] is Ji_mcm in component Mcm_a (dimensionless).
 * CONSTANTS[12] is Ja_mcm in component Mcm_a (dimensionless).
 * CONSTANTS[13] is ki_mcm in component Mcm_a (first_order_rate_constant).
 * CONSTANTS[14] is ka_mcm in component Mcm_a (first_order_rate_constant).
 * ALGEBRAIC[3] is Mcm in component Mcm (dimensionless).
 * CONSTANTS[15] is ks_sic in component Sic1 (first_order_rate_constant).
 * STATES[10] is Mih1_a in component Mih1_a (dimensionless).
 * CONSTANTS[16] is Ji_mih in component Mih1_a (dimensionless).
 * CONSTANTS[17] is Ja_mih in component Mih1_a (dimensionless).
 * CONSTANTS[18] is Vi_mih in component Mih1_a (first_order_rate_constant).
 * CONSTANTS[19] is Va_mih in component Mih1_a (first_order_rate_constant).
 * ALGEBRAIC[2] is Mih1 in component Mih1 (dimensionless).
 * STATES[11] is IE_a in component IE_a (dimensionless).
 * CONSTANTS[20] is Ji_ie in component IE_a (dimensionless).
 * CONSTANTS[21] is Ja_ie in component IE_a (dimensionless).
 * CONSTANTS[22] is ki_ie in component IE_a (first_order_rate_constant).
 * CONSTANTS[23] is ka_ie in component IE_a (first_order_rate_constant).
 * ALGEBRAIC[0] is IE in component IE (dimensionless).
 * CONSTANTS[24] is Ji_cdc20 in component kinetic_parameters (dimensionless).
 * CONSTANTS[25] is Ja_cdc20 in component kinetic_parameters (dimensionless).
 * CONSTANTS[26] is ki_cdc20 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[27] is kd_cdc20 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[28] is ka_cdc20 in component kinetic_parameters (first_order_rate_constant).
 * STATES[12] is Cdc20 in component Cdc20 (dimensionless).
 * CONSTANTS[29] is ks_cdc20_1 in component Cdc20 (first_order_rate_constant).
 * CONSTANTS[30] is ks_cdc20_2 in component Cdc20 (first_order_rate_constant).
 * CONSTANTS[31] is Js_cdc20 in component Cdc20 (dimensionless).
 * CONSTANTS[32] is Ji_cdh in component Cdh1_a (dimensionless).
 * CONSTANTS[33] is Ja_cdh in component Cdh1_a (dimensionless).
 * CONSTANTS[34] is ki_cdh in component Cdh1_a (first_order_rate_constant).
 * CONSTANTS[35] is ka_cdh_1 in component Cdh1_a (first_order_rate_constant).
 * CONSTANTS[36] is ki_cdh_1 in component Cdh1_a (first_order_rate_constant).
 * CONSTANTS[37] is ka_cdh_2 in component Cdh1_a (first_order_rate_constant).
 * ALGEBRAIC[1] is Cdh1 in component Cdh1 (dimensionless).
 * CONSTANTS[38] is ks_cln in component Cln (first_order_rate_constant).
 * CONSTANTS[39] is kd_cln in component Cln (first_order_rate_constant).
 * STATES[13] is SBF_a in component SBF_a (dimensionless).
 * CONSTANTS[40] is Ji_sbf in component SBF_a (dimensionless).
 * CONSTANTS[41] is Ja_sbf in component SBF_a (dimensionless).
 * CONSTANTS[42] is ki_sbf_1 in component SBF_a (first_order_rate_constant).
 * CONSTANTS[43] is ka_sbf_1 in component SBF_a (first_order_rate_constant).
 * CONSTANTS[44] is ki_sbf_2 in component SBF_a (first_order_rate_constant).
 * CONSTANTS[45] is ka_sbf_2 in component SBF_a (first_order_rate_constant).
 * ALGEBRAIC[4] is SBF in component SBF (dimensionless).
 * STATES[14] is Swe1 in component Swe1 (dimensionless).
 * CONSTANTS[46] is ks_swe in component Swe1 (first_order_rate_constant).
 * CONSTANTS[47] is ks_sweC in component Swe1 (first_order_rate_constant).
 * CONSTANTS[48] is khsl1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[49] is khsl1r in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[50] is kd_swe_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[51] is Ji_wee in component kinetic_parameters (dimensionless).
 * CONSTANTS[52] is Ja_wee in component kinetic_parameters (dimensionless).
 * CONSTANTS[53] is Vi_wee in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[54] is Va_wee in component kinetic_parameters (first_order_rate_constant).
 * ALGEBRAIC[6] is BUD in component BUD (dimensionless).
 * STATES[15] is PSwe1 in component PSwe1 (dimensionless).
 * STATES[16] is Swe1M in component Swe1M (dimensionless).
 * STATES[17] is PSwe1M in component PSwe1M (dimensionless).
 * CONSTANTS[55] is kd_swe_2 in component PSwe1M (first_order_rate_constant).
 * STATES[18] is BE in component BE (dimensionless).
 * CONSTANTS[56] is ks_bud in component BE (first_order_rate_constant).
 * CONSTANTS[57] is kd_bud in component BE (first_order_rate_constant).
 * CONSTANTS[58] is mu in component M (first_order_rate_constant).
 * CONSTANTS[59] is IE_total in component IE (dimensionless).
 * CONSTANTS[60] is Cdh1_total in component Cdh1 (dimensionless).
 * CONSTANTS[61] is Mih1_total in component Mih1 (dimensionless).
 * CONSTANTS[62] is Mcm_total in component Mcm (dimensionless).
 * CONSTANTS[63] is SBF_total in component SBF (dimensionless).
 * ALGEBRAIC[5] is Swe1_total in component Swe1_total (dimensionless).
 * CONSTANTS[64] is kswe_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[65] is kswe_2 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[66] is kswe_3 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[67] is kmih_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[68] is kmih_2 in component kinetic_parameters (first_order_rate_constant).
 * RATES[0] is d/dt Clb2 in component Clb2 (dimensionless).
 * RATES[6] is d/dt PClb2 in component PClb2 (dimensionless).
 * RATES[7] is d/dt Trim in component Trim (dimensionless).
 * RATES[9] is d/dt PTrim in component PTrim (dimensionless).
 * RATES[2] is d/dt Mcm_a in component Mcm_a (dimensionless).
 * RATES[5] is d/dt Sic1 in component Sic1 (dimensionless).
 * RATES[10] is d/dt Mih1_a in component Mih1_a (dimensionless).
 * RATES[11] is d/dt IE_a in component IE_a (dimensionless).
 * RATES[4] is d/dt Cdc20_a in component Cdc20_a (dimensionless).
 * RATES[12] is d/dt Cdc20 in component Cdc20 (dimensionless).
 * RATES[3] is d/dt Cdh1_a in component Cdh1_a (dimensionless).
 * RATES[8] is d/dt Cln in component Cln (dimensionless).
 * RATES[13] is d/dt SBF_a in component SBF_a (dimensionless).
 * RATES[14] is d/dt Swe1 in component Swe1 (dimensionless).
 * RATES[15] is d/dt PSwe1 in component PSwe1 (dimensionless).
 * RATES[16] is d/dt Swe1M in component Swe1M (dimensionless).
 * RATES[17] is d/dt PSwe1M in component PSwe1M (dimensionless).
 * RATES[18] is d/dt BE in component BE (dimensionless).
 * RATES[1] is d/dt M in component M (dimensionless).
 * There are a total of 2 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 0.184;
CONSTANTS[0] = 0.5;
CONSTANTS[1] = 10;
CONSTANTS[2] = 0.015;
CONSTANTS[3] = 0.015;
CONSTANTS[4] = 1;
CONSTANTS[5] = 0.1;
CONSTANTS[6] = 300;
CONSTANTS[7] = 0.1;
CONSTANTS[8] = 0.01;
CONSTANTS[9] = 1;
CONSTANTS[10] = 3;
STATES[1] = 0.802;
STATES[2] = 0.933;
STATES[3] = 0.993;
STATES[4] = 1.438;
STATES[5] = 0.003;
STATES[6] = 0;
STATES[7] = 0.084;
STATES[8] = 0.054;
STATES[9] = 0;
CONSTANTS[11] = 0.1;
CONSTANTS[12] = 0.1;
CONSTANTS[13] = 0.15;
CONSTANTS[14] = 1;
CONSTANTS[15] = 0.1;
STATES[10] = 0.808;
CONSTANTS[16] = 0.1;
CONSTANTS[17] = 0.1;
CONSTANTS[18] = 0.3;
CONSTANTS[19] = 1;
STATES[11] = 0.522;
CONSTANTS[20] = 0.01;
CONSTANTS[21] = 0.01;
CONSTANTS[22] = 0.04;
CONSTANTS[23] = 0.1;
CONSTANTS[24] = 0.001;
CONSTANTS[25] = 0.001;
CONSTANTS[26] = 0.25;
CONSTANTS[27] = 0.1;
CONSTANTS[28] = 1;
STATES[12] = 1.172;
CONSTANTS[29] = 0.005;
CONSTANTS[30] = 0.3;
CONSTANTS[31] = 0.3;
CONSTANTS[32] = 0.01;
CONSTANTS[33] = 0.01;
CONSTANTS[34] = 35;
CONSTANTS[35] = 1;
CONSTANTS[36] = 2;
CONSTANTS[37] = 10;
CONSTANTS[38] = 0.1;
CONSTANTS[39] = 0.1;
STATES[13] = 0.124;
CONSTANTS[40] = 0.01;
CONSTANTS[41] = 0.01;
CONSTANTS[42] = 1;
CONSTANTS[43] = 1;
CONSTANTS[44] = 2;
CONSTANTS[45] = 0;
STATES[14] = 0;
CONSTANTS[46] = 0.0025;
CONSTANTS[47] = 0;
CONSTANTS[48] = 1;
CONSTANTS[49] = 0.01;
CONSTANTS[50] = 0.007;
CONSTANTS[51] = 0.05;
CONSTANTS[52] = 0.05;
CONSTANTS[53] = 1;
CONSTANTS[54] = 0.3;
STATES[15] = 0;
STATES[16] = 0.018;
STATES[17] = 0.013;
CONSTANTS[55] = 0.05;
STATES[18] = 0;
CONSTANTS[56] = 0.1;
CONSTANTS[57] = 0.1;
CONSTANTS[58] = 0.005;
CONSTANTS[59] = 1;
CONSTANTS[60] = 1;
CONSTANTS[61] = 1;
CONSTANTS[62] = 1;
CONSTANTS[63] = 1;
CONSTANTS[64] = 2;
CONSTANTS[65] = 0.01;
CONSTANTS[66] = 0.2;
CONSTANTS[67] = 5;
CONSTANTS[68] = 0.5;
RATES[0] = 0.1001;
RATES[6] = 0.1001;
RATES[7] = 0.1001;
RATES[9] = 0.1001;
RATES[2] = 0.1001;
RATES[5] = 0.1001;
RATES[10] = 0.1001;
RATES[11] = 0.1001;
RATES[4] = 0.1001;
RATES[12] = 0.1001;
RATES[3] = 0.1001;
RATES[8] = 0.1001;
RATES[13] = 0.1001;
RATES[14] = 0.1001;
RATES[15] = 0.1001;
RATES[16] = 0.1001;
RATES[17] = 0.1001;
RATES[18] = 0.1001;
RATES[1] = 0.1001;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[0] - (( CONSTANTS[2]*(CONSTANTS[0]+STATES[2])*STATES[1])/(1.00000+STATES[1]/CONSTANTS[1])+ ALGEBRAIC[7]*STATES[6]+ CONSTANTS[7]*STATES[7]+ (CONSTANTS[8]+ CONSTANTS[9]*STATES[8]+ CONSTANTS[10]*STATES[0])*STATES[7]) - ( (CONSTANTS[3]+ CONSTANTS[4]*STATES[3]+ CONSTANTS[5]*STATES[4])*STATES[0]+ ALGEBRAIC[8]*STATES[0]+ CONSTANTS[6]*STATES[5]*STATES[0]);
resid[1] = RATES[6] - ( ALGEBRAIC[8]*STATES[0]+ CONSTANTS[7]*STATES[9]+ (CONSTANTS[8]+ CONSTANTS[9]*STATES[8]+ CONSTANTS[10]*STATES[0])*STATES[9]) - ( (CONSTANTS[3]+ CONSTANTS[4]*STATES[3]+ CONSTANTS[5]*STATES[4])*STATES[6]+ ALGEBRAIC[7]*STATES[6]+ CONSTANTS[6]*STATES[5]*STATES[6]);
resid[2] = RATES[7] - ( CONSTANTS[6]*STATES[5]*STATES[0]+ ALGEBRAIC[7]*STATES[9]) - ( CONSTANTS[7]*STATES[7]+ (CONSTANTS[8]+ CONSTANTS[9]*STATES[8]+ CONSTANTS[10]*STATES[0])*STATES[7]+ (CONSTANTS[3]+ CONSTANTS[4]*STATES[3]+ CONSTANTS[5]*STATES[4])*STATES[7]+ ALGEBRAIC[8]*STATES[7]);
resid[3] = RATES[9] - ( ALGEBRAIC[8]*STATES[7]+ CONSTANTS[6]*STATES[5]*STATES[6]) - ( CONSTANTS[7]*STATES[9]+ (CONSTANTS[8]+ CONSTANTS[9]*STATES[8]+ CONSTANTS[10]*STATES[0])*STATES[9]+ (CONSTANTS[3]+ CONSTANTS[4]*STATES[3]+ CONSTANTS[5]*STATES[4])*STATES[9]+ ALGEBRAIC[7]*STATES[9]);
resid[4] = RATES[2] - ( - CONSTANTS[13]*STATES[2])/(CONSTANTS[11]+STATES[2])+( CONSTANTS[14]*ALGEBRAIC[3]*STATES[0])/(CONSTANTS[12]+ALGEBRAIC[3]);
resid[5] = RATES[5] - (CONSTANTS[15]+ CONSTANTS[7]*(STATES[9]+STATES[7])+ (CONSTANTS[3]+ CONSTANTS[4]*STATES[3]+ CONSTANTS[5]*STATES[4])*(STATES[9]+STATES[7])) - ( (CONSTANTS[8]+ CONSTANTS[9]*STATES[8]+ CONSTANTS[10]*STATES[0])*STATES[5]+ CONSTANTS[6]*STATES[5]*(STATES[0]+STATES[6]));
resid[6] = RATES[10] - ( - CONSTANTS[18]*STATES[10])/(CONSTANTS[16]+STATES[10])+( CONSTANTS[19]*STATES[0]*ALGEBRAIC[2])/(CONSTANTS[17]+ALGEBRAIC[2]);
resid[7] = RATES[11] - ( - CONSTANTS[22]*STATES[11])/(CONSTANTS[20]+STATES[11])+( CONSTANTS[23]*STATES[0]*ALGEBRAIC[0])/(CONSTANTS[21]+ALGEBRAIC[0]);
resid[8] = RATES[4] - ( CONSTANTS[28]*STATES[11]*STATES[12])/(CONSTANTS[25]+STATES[12]) - (( CONSTANTS[26]*STATES[4])/(CONSTANTS[24]+STATES[4])+ CONSTANTS[27]*STATES[4]);
resid[9] = RATES[12] - (CONSTANTS[29]+( CONSTANTS[30]*pow(STATES[0], 4.00000))/(pow(CONSTANTS[31], 4.00000)+pow(STATES[0], 4.00000))+( CONSTANTS[26]*STATES[4])/(CONSTANTS[24]+STATES[4])) - (( CONSTANTS[28]*STATES[11]*STATES[12])/(CONSTANTS[25]+STATES[12])+ CONSTANTS[27]*STATES[12]);
resid[10] = RATES[3] - ( - ( CONSTANTS[34]*STATES[0]+ CONSTANTS[36]*STATES[8])*STATES[3])/(CONSTANTS[32]+STATES[3])+( (CONSTANTS[35]+ CONSTANTS[37]*STATES[4])*ALGEBRAIC[1])/(CONSTANTS[33]+ALGEBRAIC[1]);
resid[11] = RATES[8] -  CONSTANTS[38]*STATES[13] -  CONSTANTS[39]*STATES[8];
resid[12] = RATES[13] - ( - (CONSTANTS[42]+ CONSTANTS[44]*STATES[0])*STATES[13])/(CONSTANTS[40]+STATES[13])+( ( CONSTANTS[43]*STATES[1]+ CONSTANTS[45]*STATES[8])*ALGEBRAIC[4])/(CONSTANTS[41]+ALGEBRAIC[4]);
resid[13] = RATES[14] - ( CONSTANTS[46]*STATES[13]+CONSTANTS[47]+ CONSTANTS[49]*STATES[16]+( CONSTANTS[54]*STATES[15])/(CONSTANTS[52]+STATES[15])) - ( CONSTANTS[48]*ALGEBRAIC[6]*STATES[14]+( CONSTANTS[53]*STATES[0]*STATES[14])/(CONSTANTS[51]+STATES[14])+ CONSTANTS[50]*STATES[14]);
resid[14] = RATES[15] - ( CONSTANTS[49]*STATES[17]+( CONSTANTS[53]*STATES[14]*STATES[0])/(CONSTANTS[51]+STATES[14])) - ( CONSTANTS[48]*ALGEBRAIC[6]*STATES[15]+( CONSTANTS[54]*STATES[15])/(CONSTANTS[52]+STATES[15])+ CONSTANTS[50]*STATES[15]);
resid[15] = RATES[16] - ( CONSTANTS[48]*ALGEBRAIC[6]*STATES[14]+( CONSTANTS[54]*STATES[17])/(CONSTANTS[52]+STATES[17])) - ( CONSTANTS[49]*STATES[16]+( CONSTANTS[53]*STATES[0]*STATES[16])/(CONSTANTS[51]+STATES[16])+ CONSTANTS[50]*STATES[16]);
resid[16] = RATES[17] - ( CONSTANTS[48]*ALGEBRAIC[6]*STATES[15]+( CONSTANTS[53]*STATES[0]*STATES[16])/(CONSTANTS[51]+STATES[16])) - ( CONSTANTS[49]*STATES[17]+( CONSTANTS[54]*STATES[17])/(CONSTANTS[52]+STATES[17])+ CONSTANTS[55]*STATES[17]);
resid[17] = RATES[18] -  CONSTANTS[56]*STATES[8] -  CONSTANTS[57]*STATES[18];
resid[18] = RATES[1] -  CONSTANTS[58]*STATES[1];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[5] = STATES[14]+STATES[15]+STATES[16]+STATES[17];
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = CONSTANTS[59] - STATES[11];
ALGEBRAIC[1] = CONSTANTS[60] - STATES[3];
ALGEBRAIC[2] = CONSTANTS[61] - STATES[10];
ALGEBRAIC[3] = CONSTANTS[62] - STATES[2];
ALGEBRAIC[4] = CONSTANTS[63] - STATES[13];
ALGEBRAIC[6] = (CONDVAR[0]<=0.00000&&CONDVAR[1]<0.00000 ? 0.00000 : 1.00000);
ALGEBRAIC[7] =  CONSTANTS[67]*STATES[10]+ CONSTANTS[68]*ALGEBRAIC[2];
ALGEBRAIC[8] =  CONSTANTS[64]*STATES[14]+ CONSTANTS[65]*STATES[16]+ CONSTANTS[66]*STATES[15];
}
void
getStateInformation(double* SI)
{
SI[0] = 1.0;
SI[1] = 1.0;
SI[2] = 1.0;
SI[3] = 1.0;
SI[4] = 1.0;
SI[5] = 1.0;
SI[6] = 1.0;
SI[7] = 1.0;
SI[8] = 1.0;
SI[9] = 1.0;
SI[10] = 1.0;
SI[11] = 1.0;
SI[12] = 1.0;
SI[13] = 1.0;
SI[14] = 1.0;
SI[15] = 1.0;
SI[16] = 1.0;
SI[17] = 1.0;
SI[18] = 1.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = STATES[18] - 0.600000;
CONDVAR[1] = STATES[0] - 0.200000;
}